Sam Smith (@scolbysmith)
Activity by Sam Smith
ROCHESTER, Minn. — Feb. 24, 2014 — Mayo Clinic researchers have fashioned a new key to unlocking the secrets of the human genome. The Binary Indexing Mapping Algorithm, version 3 (BIMA V3) is a freely available computer algorithm that identifies alterations in tumor genomes up to 20 times faster and with 25 percent greater accuracy than other popular genomic alignment programs. BIMA results are published this month in the journal Bioinformatics.
Journalists: Sound bites with Dr. Vasmatzis are available in the downloads.
BIMA is a next-generation sequencing mapping and alignment algorithm, customized to process mate pair library sequencing. Mate pair sequencing is a comprehensive and cost-effective method for detecting changes throughout the entire genome.
“BIMA allows us to evaluate tumor genomes in a fraction of the time it takes many popular technologies,” says George Vasmatzis, Ph.D., a Mayo Clinic molecular biologist, director of the Biomarker Discovery Program in the Mayo Clinic Center for Individualized Medicine, and senior author of the paper. “We believe this tool will lead to a better understanding of tumor genomics, and ultimately better therapy for patients with cancer.”
Study targets EGFR and FGFR cellular pathways to treat rare disease
SCOTTSDALE, Ariz. — Feb. 13, 2014 — Physicians at Mayo Clinic’s Center for Individualized Medicine and researchers at the Translational Genomics Research Institute (TGen) have personalized drug treatments for patients with cholangiocarcinoma using genomic sequencing technologies. Potential new treatment approaches are being validated to develop new tests that physicians can use to guide therapy for this aggressive cancer of the bile ducts that progresses quickly and is difficult to treat.
Clinically important findings suggest that targeting the epidermal growth factor receptor (EGFR) and the fibroblast growth factor receptor (FGFR) cellular pathways may benefit thousands of patients with this disease, [...]
ROCHESTER, Minn. ― Jan. 21, 2014 ― Researchers at Mayo Clinic have found amplification of HER2, a known driver of some breast cancers, in a type of bladder cancer called micropapillary urothelial carcinoma (MPUC) and have shown that the presence of HER2 amplification is associated with particularly aggressive tumors. These findings suggest that administering trastuzumab to MPUC patients with HER2 amplification could improve outcomes, just as it has for breast cancer. The study is published in this month’s Modern Pathology.
Journalists: B-roll of images and sound bites with Dr. Cheville are available in the downloads.
As with breast cancer, HER2 amplification in MPUC results in a faster growing form of cancer that spreads quickly and has a higher chance of recurrence. The hope is that combating this amplification with trastuzumab,
Two-year study of Plavix and Brilinta to include approximately 5,300 patients from 15 hospitals worldwide; participant DNA biobank to help elucidate genomics of coronary artery disease
ROCHESTER, Minn. — Which antiplatelet medication is best after a coronary stent? The costly and potential life-or-death question lingers after most of the 600,000 angioplasties performed every year in the United States. The answer may lie in your genes, but professional cardiovascular societies and many working cardiologists question the U.S. Food and Drug Administration's recent recommendation that patients undergo genetic testing before taking Plavix (clopidogrel bisulfate).
ROCHESTER, Minn. — A new study at Mayo Clinic is using genomic sequencing to develop customized treatments for men with castration-resistant prostate cancer, a progressive and incurable stage of prostate cancer, which no longer responds to hormone therapies that stop or slow testosterone production.
"Men with castration-resistant prostate cancer have abysmal survival rates, typically living an average of two years once hormone therapies fail," says Manish Kohli, M.D., a Mayo Clinic oncologist and principal investigator of the Prostate Cancer Medically Optimized Genome-Enhanced Therapy (PROMOTE) study. Dr. Kohli says the poor prognosis for men with this cancer highlights the need for studies like PROMOTE, which seek to match new targeted drugs with the genomic characteristics of individual patients' tumors.
Several new therapies have recently been approved by the FDA for use in treating castration-resistant prostate cancer, offering new hope for men with this disease. However, many questions remain over which medications to use in individual cases. In the PROMOTE study, researchers and doctors are using exome sequencing and RNA profiling to identify molecular fingerprints within prostate cancers that can be used to identify the optimal drug for the individual patient.
In addition to identifying individualized treatment plans, PROMOTE will uncover new targets in the cancer genome that investigators and drug companies can use to develop new therapies. These new targets will be identified largely through mouse "avatars," which will carry the individual tumors of PROMOTE study participants. These avatar mice also will help doctors identify and test new drugs against the patients' tumors before introducing the toxic and potentially harmful agents into the patients, themselves.
"The approach we are taking with PROMOTE is exactly what we are working toward across Mayo Clinic through our Center for Individualized Medicine," says Gianrico Farrugia, M.D., director of the Mayo Clinic Center for Individualized Medicine. "We're offering individualized care and tailored treatment options for our patients."
Prostate cancer is the most commonly diagnosed solid organ malignancy in the U.S with more than 238,000 new diagnoses annually and an estimated 29,720 deaths. It is the second leading cause of cancer deaths among American men, according to the Surveillance Epidemiology and End Results Program of the National Cancer Institute.
The PROMOTE study is a collaboration of the Mayo Clinic Center for Individualized Medicine and the Mayo Clinic Cancer Center. For more information about enrollment in PROMOTE contact 507-284-3067.
The Center for Individualized Medicine discovers and integrates the latest in genomic, molecular and clinical sciences into personalized care for each Mayo Clinic patient. Visit http://mayoresearch.mayo.edu/mayo/research/center-for-individualized-medicine/ for more information.
ROCHESTER, Minn. — September 20, 2012. The Individualizing Medicine 2012: Transforming Patient Care with Genomics conference, scheduled for Oct. 1-3, will be webcast live for journalists on the Mayo Clinic News Network. This inaugural conference from Mayo's Center for Individualized Medicine focuses on the promise and challenges of incorporating genomics into patient care. All conference content, including presentations and panel discussions, will be available to journalists via the Mayo Clinic News Network. Media professionals interested in watching the conference webcast must go to the News Network web site to sign up and set a username and password; registration is free.
Individualizing Medicine 2012 covers five key themes on use of genomics in patient care. Each theme consists of three presentations, followed by a panel discussion. Schedule highlights include:
Other conference highlights include the media panel titled "Great Expectations: Making Informed Decisions in Individualized Medicine." Ira Flatow, host of NPR's "Science Friday," will moderate the discussion, which focuses on the perceptions and realities of genomics in patient care. The panel is scheduled from 7-8 p.m., Oct. 2 at the Mayo Civic Center in Rochester. The panel will be webcast live on Mayo Clinic's Advancing the Science blog. Viewers may submit questions during the event to firstname.lastname@example.org.
Panelists scheduled to appear include:
ROCHESTER, Minn. — August 13, 2012. Mayo Clinic's Individualizing Medicine Conference, scheduled for
Oct. 1–3, will draw experts from around the world to discuss the use of genomics in patient care.
Physicians and researchers in this rapidly growing field are building a new type of medicine based on the genomic and molecular interactions that make each patient unique. At Mayo Clinic, the Center for Individualized Medicine is making these discoveries and building a clinical practice that delivers genomic medicine as part of routine care.
MULTIMEDIA ALERT: Multimedia resources, including video of Dr. Farrugia, are available for download on the Mayo Clinic News Network.
Conference sessions will be accessible to journalists through the News Network. Media may register for the site here.
This inaugural conference, Individualizing Medicine 2012, will be held at the Mayo Civic Center in Rochester. Presentations will range from cutting-edge diagnostics and experimental cancer treatments to the most ethical and respectful ways to manage patient genomic information. An introduction to individualized medicine will be presented for those unfamiliar with the field.
"The technologies of genome sequencing have made tremendous strides over the past few years. The time needed to sequence and interpret whole genomes is no longer the seemingly insurmountable barrier it once was due to the use of these tools in the everyday care of our patients," says Gianrico Farrugia, M.D., director of Mayo Clinic's Center for Individualized Medicine, which is holding the event.
"Right now, we are building genomics technologies into our laboratories and electronic medical records," Dr. Farrugia says. "This conference will be a place for both doctors and scientists to develop real-world strategies for incorporating genomics into the clinical practice."
Conference highlights include:
ROCHESTER, Minn. — July 31, 2012. Researchers at Mayo Clinic have completed the world's first genome-wide sequencing analysis of peripheral T-cell lymphomas, unlocking the genetic secrets of this poorly understood and highly aggressive cancer of the immune system.
Andrew Feldman, M.D., a Mayo Clinic pathologist and Damon Runyun Clinical Investigator, and a team of researchers affiliated with Mayo's Center for Individualized Medicine and Mayo Clinic Cancer Center, found 13 genomic abnormalities that were seen in multiple peripheral T-cell lymphomas. Of particular interest, five of these abnormalities relate to production and behavior of the p53 protein — often called the "guardian of the genome" because of the central role it plays in regulating cell life cycles and, therefore, suppressing cancers.
The study, entitled "Genome-wide Analysis Reveals Recurrent Structural Abnormalities of TP63 and other p53-related Genes in Peripheral T-cell Lymphomas," is scheduled for early release in the online edition of the journal Blood at 9 a.m. on Wednesday, Aug. 1, 2012.
"Every time I diagnose a peripheral T-cell lymphoma, I know that two out of three patients will succumb to that lymphoma," says Dr. Feldman. "That's a very unsatisfying feeling, and I hope that our research can help change those statistics."
Peripheral T-cell lymphomas account for about 12 percent of non-Hodgkin's lymphomas and carry remarkably high mortality rates. Fewer than 35 percent of patients live five years beyond diagnosis.
New diagnostic biomarkers (chemical or genetic clues in the body's system) and treatments aimed at specific subgroups of peripheral T-cell lymphomas could lead to improved outcomes, says Dr. Feldman. Developing these, however, has been a challenge for several reasons. Lymphomas that look remarkably similar under a microscope may differ substantially in their overall prognoses and responses to treatment. Additionally, scientists and doctors have a relatively poor understanding of how peripheral T-cell lymphomas develop and proliferate.
"The most common type of T-cell lymphoma is called 'not otherwise specified.' It's basically a wastebasket diagnosis because we don't understand enough about the specific genetic abnormalities to be able to pinpoint subtypes of T-cell lymphomas that might trigger different treatments by the treating oncologist," says Dr. Feldman.
Dr. Feldman's study will be used to improve diagnostic tests and develop targeted treatments for peripheral T-cell lymphoma.
ROCHESTER, Minn. — June 11, 2012. The billions of bugs in our guts have a newfound role: regulating the immune system and related autoimmune diseases such as rheumatoid arthritis, according to researchers at Mayo Clinic and the University of Illinois at Urbana-Champaign.
Larger-than-normal populations of specific gut bacteria may trigger the development of diseases like rheumatoid arthritis and possibly fuel disease progression in people genetically predisposed to this crippling and confounding condition, say the researchers, who are participating in the Mayo Illinois Alliance for Technology Based Healthcare.
The study is published in the April 2012 issue of PloS ONE.
"A lot of people suspected that gut flora played a role in rheumatoid arthritis, but no one had been able to prove it because they couldn't say which came first — the bacteria or the genes," says senior author Veena Taneja, Ph.D., a Mayo Clinic immunologist. "Using genomic sequencing technologies, we have been able to show the gut microbiome may be used as a biomarker for predisposition."
The roughly 10 trillion cells that make up the human body have neighbors: mostly bacteria that often help, training the immune system and aiding in digestion, for example. The bacteria in the intestines, in addition to a relatively small number of other microorganisms (the gut microbiome), outnumber human cells 10-to-1.
Researchers found that hormones and changes related to aging may further modulate the gut immune system and exacerbate inflammatory conditions in genetically susceptible individuals.
Nearly 1 percent of the world's population has rheumatoid arthritis, a disease in which the immune system attacks tissues, inflaming joints and sometimes leading to deadly complications such as heart disease. Other diseases with suspected gut bacterial ties include type I diabetes and multiple sclerosis.
Researchers with the Mayo Illinois Alliance for Technology Based Healthcare say that identifying new biomarkers in intestinal microbial populations and maintaining a balance in gut bacteria could help physicians stop rheumatoid arthritis before it starts.
"This study is an important advance in our understanding of the immune system disturbances associated with rheumatoid arthritis. While we do not yet know what the causes of this disease are, this study provides important insights into the immune system and its relationship to bacteria of the gut, and how these factors may affect people with genetic susceptibilities to disease," says Eric Matteson, M.D., chairman of rheumatology at Mayo Clinic, who was not a study author.